Chapter 3 Protein Structure and Function What Are the Building Blocks of Proteins Primary Structure A protein s primary structure is its unique sequence of amino acids Because the amino acid R groups affect a polypeptide s properties and function just a single amino acid change can radically alter protein function Tertiary Structure The tertiary structure of a polypeptide results from interactions between R groups or between R groups and the peptide backbone These contacts cause the backbone to bend and fold and contribute to the distinctive shape of the polypeptide R group interactions include hydrogen bonds hydrophobic interactions van der Waals interactions covalent disulfide bonds and ionic bonds Tertiary structures of proteins results from interactions with R groups Summary of R group Interactions That Form Tertiary Structures form between hydrogen atoms and the carbonyl group in the peptide bonded backbone and between hydrogen and negatively charged atoms in side chains within a protein increase stability of surrounding water molecules by increasing hydrogen bonding are weak electrical interactions between hydrophobic side chains form between sulfur containing R groups form between groups that have full and opposing charges Quaternary Structure Combinations of polypetide subunits combinations of tertiary structures May be held together by bonds or other interactions among R groups Proteins can be a dimer a tetramer etc All three higher level structures are based on Summary of Protein Structure Note that protein structure is structure is based on structure which is based in part on structure All three of the higher level structures are based on primary structure The combined effects of primary secondary tertiary and sometimes quaternary structure allow for amazing diversity in protein form and function Structure Defines Function Proteins fold into their normal shape What happens proteins don t fold properly Prions are improperly folded proteins Enzymes Enzymes are and typically catalyze only one reaction Most biological chemical reactions occur at meaningful rates only in the presence of an enzyme Enzymes do two things 1 2 Protein catalysts are important because they speed up the chemical reactions that are required for life How Do Enzymes Work Enzymes bring together in specific positions that facilitate reactions and are very specific in which reactions they catalyze Substrates bind to the enzyme s Many enzymes undergo a conformational change when the substrates are bound to the active site this change is called an Interactions between the enzyme and the substrate stabilize the transition state and lower the activation energy required for the reaction to proceed Catalysts and Free Energy A is a substance that lowers the activation energy of a reaction and increases the rate of the reaction Catalysts lower the activation energy of a reaction by lowering the free energy of the Catalysts do not change G and are not consumed in the reaction Enzymes have active sites Conformational change in protein shape results in induced fit Enzymes bring reactants together in precise orientations and stabilize transition states Protein catalysts speed up chemical reactions that are required for life occurs when a molecule similar in size and shape to the substrate competes with the substrate for access to the active site occurs when a molecule causes a change in enzyme shape by binding to the enzyme at a location other than the active site Allosteric regulation can activate or deactivate the enzyme
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